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# Serialized Form

Package org.metaqtl

Class org.metaqtl.EMCriteria extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

### aic

    double aic

### aicc

    double aicc

### aic3

    double aic3

### bic

    double bic

### mir

    double mir

### icomp

    double icomp

### awe

    double awe

Class org.metaqtl.Qtl.QTLCross extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

### name

    java.lang.String name

  The name of the cross design.

### type

    int type

  The type of the cross.

### gen

    int gen

  The number of generations.

### size

    int size

  The number of individuals.

Class org.metaqtl.Qtl.QTLProj extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

### mapOrigin

    java.lang.String mapOrigin

  The name of the map from which this QTL comes.

### o_mrkIdxL

    int o_mrkIdxL

  The original indice of the left flanking marker.

### o_mrkIdxR

    int o_mrkIdxR

  The original indice of the right flanking marker.

### s_mrkIdxL

    int s_mrkIdxL

  The skeleton indice of the left flanking marker.

### s_mrkIdxR

    int s_mrkIdxR

  The skeleton indice of the right flanking marker.

### mapScale

    double mapScale

  The scale ratio between the original map and the map on which the QTL has been projected.

### mapWeight

    double mapWeight

  The cumulated scale weights of the common marke sequences between the original map and the map on which the QTL has been projected.

### intScale

    double intScale

  The scale ratio between the original flanking marker interval and the one on the map used for projection.

### shareFlanking

    boolean shareFlanking

  True if the two maps share a common marker sequence around the QTL.

### swap

    boolean swap

  True if the flanking marker order are inversed between the skeleton and the original map.

Class org.metaqtl.Qtl.QTLStats extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

### rsquare

    double rsquare

  The r-square, i.e the proportion of variance explained by the QTL.

### additive

    double additive

  The additive effect of the QTL.

### dominance

    double dominance

  The dominance effect of the QTL.

### lod

    double lod

  The lod score of the QTL.

Class org.metaqtl.Qtl.QTLSupport extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

### ic1

    double ic1

  The recombination rate between the QTL position and the left border of the IC.

### ic2

    double ic2

  The recombination rate between the QTL position and the right border of the IC.

### from

    double from

  The position from the first marker to the left border of the IC.

### to

    double to

  The position from the first marker to the right border of the IC.

### lodDecrease

    double lodDecrease

  The value of the LOD decrease used to obtain the CI.

Class org.metaqtl.Qtl.QTLTrait extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

### name

    java.lang.String name

  The name of the trait.

### unit

    java.lang.String unit

  The unit of the trait.

### group

    java.lang.String group

  The name of the group to which the trait belongs.

Class org.metaqtl.TreeNode extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

### idx

    int idx

  ? The identifiant of the cluster.

### label

    java.lang.String label

  The label of the cluster

### card

    int card

  The number of sequences in the cluster

### nidx

    int[] nidx

  The indices of the sub-nodes

### leaf

    boolean leaf

  The status of the node.

### dist

    double dist

  The distance between the node and its parent.

### height

    double height

  The distance between the node and the root of the tree (if defined).

### children

    TreeNode[] children

  Left and right children, or null

### parent

    TreeNode parent

  The parent of the node

### x

    double x

### y

    double y

### xc

    double xc

Package org.metaqtl.bio.entity

Class org.metaqtl.bio.entity.BioEntityCollection extends java.util.ArrayList implements Serializable

serialVersionUID: 1L

Serialized Fields

### name

    java.lang.String name

### parent

    IBioEntity parent

### properties

    java.util.Properties properties

Package org.metaqtl.main

Class org.metaqtl.main.CmdLineParser.IllegalOptionValueException extends CmdLineParser.OptionException implements Serializable

Serialized Fields

### option

    CmdLineParser.Option option

### value

    java.lang.String value

Class org.metaqtl.main.CmdLineParser.NotFlagException extends CmdLineParser.UnknownOptionException implements Serializable

Serialized Fields

### notflag

    char notflag

Class org.metaqtl.main.CmdLineParser.OptionException extends java.lang.Exception implements Serializable

Class org.metaqtl.main.CmdLineParser.UnknownOptionException extends CmdLineParser.OptionException implements Serializable

Serialized Fields

### optionName

    java.lang.String optionName

Class org.metaqtl.main.CmdLineParser.UnknownSuboptionException extends CmdLineParser.UnknownOptionException implements Serializable

Serialized Fields

### suboption

    char suboption

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